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PatrickMcSweeny's solution

to Hamming in the JavaScript Track

Published at Aug 24 2019 · 0 comments
Instructions
Test suite
Solution

Calculate the Hamming Distance between two DNA strands.

Your body is made up of cells that contain DNA. Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells. In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!

When cells divide, their DNA replicates too. Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information. If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred. This is known as the "Hamming Distance".

We read DNA using the letters C,A,G and T. Two strands might look like this:

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

They have 7 differences, and therefore the Hamming Distance is 7.

The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)

Implementation notes

The Hamming distance is only defined for sequences of equal length, so an attempt to calculate it between sequences of different lengths should not work. The general handling of this situation (e.g., raising an exception vs returning a special value) may differ between languages.

Setup

Go through the setup instructions for Javascript to install the necessary dependencies:

https://exercism.io/tracks/javascript/installation

Requirements

Install assignment dependencies:

$ npm install

Making the test suite pass

Execute the tests with:

$ npm test

In the test suites all tests but the first have been skipped.

Once you get a test passing, you can enable the next one by changing xtest to test.

Source

The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/

Submitting Incomplete Solutions

It's possible to submit an incomplete solution so you can see how others have completed the exercise.

hamming.spec.js

import { compute } from './hamming';

describe('Hamming', () => {
  test('empty strands', () => {
    expect(compute('', '')).toEqual(0);
  });

  xtest('single letter identical strands', () => {
    expect(compute('A', 'A')).toEqual(0);
  });

  xtest('single letter different strands', () => {
    expect(compute('G', 'T')).toEqual(1);
  });

  xtest('long identical strands', () => {
    expect(compute('GGACTGAAATCTG', 'GGACTGAAATCTG')).toEqual(0);
  });

  xtest('long different strands', () => {
    expect(compute('GGACGGATTCTG', 'AGGACGGATTCT')).toEqual(9);
  });

  xtest('disallow first strand longer', () => {
    expect(() => compute('AATG', 'AAA')).toThrow(
      new Error('left and right strands must be of equal length'),
    );
  });

  xtest('disallow second strand longer', () => {
    expect(() => compute('ATA', 'AGTG')).toThrow(
      new Error('left and right strands must be of equal length'),
    );
  });

  xtest('disallow left empty strand', () => {
    expect(() => compute('', 'G')).toThrow(
      new Error('left strand must not be empty'),
    );
  });

  xtest('disallow right empty strand', () => {
    expect(() => compute('G', '')).toThrow(
      new Error('right strand must not be empty'),
    );
  });
});
export const compute = (leftStrand, rightStrand) => {
  validateStrands(leftStrand, rightStrand);

  let range = [...Array(leftStrand.length).keys()];

  return range.filter((n, i) => {
    return leftStrand[i] !== rightStrand[i];
  }).length;
};

export const validateStrands = (leftStrand, rightStrand) => {
  if (leftStrand.length === 0 && rightStrand.length > 0) {
    throw new Error("left strand must not be empty");
  }

  if (rightStrand.length === 0 && leftStrand.length > 0) {
    throw new Error("right strand must not be empty");
  }

  if (leftStrand.length !== rightStrand.length) {
    throw new Error("left and right strands must be of equal length");
  }
};

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